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- EMDB-17204: Cryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homod... -

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Basic information

Entry
Database: EMDB / ID: EMD-17204
TitleCryo-EM structure of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)
Map dataCryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA
Sample
  • Complex: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)
    • Protein or peptide: x 14 types
    • DNA: x 2 types
  • Ligand: x 3 types
KeywordsDNA Replication / DNA Replication Initiation / Replisome / DONSON / Replication
Function / homology
Function and homology information


MCM complex assembly / Unwinding of DNA / Assembly of the pre-replicative complex / Orc1 removal from chromatin / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / regulation of sister chromatid cohesion / : / replication fork arrest / gonad development ...MCM complex assembly / Unwinding of DNA / Assembly of the pre-replicative complex / Orc1 removal from chromatin / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / regulation of sister chromatid cohesion / : / replication fork arrest / gonad development / cell cycle phase transition / DNA strand elongation involved in mitotic DNA replication / nuclear DNA replication / negative regulation of DNA helicase activity / GINS complex / mitotic DNA replication preinitiation complex assembly / meiotic sister chromatid cohesion / mitotic DNA replication / DNA replication checkpoint signaling / MCM complex / DNA replication preinitiation complex / double-strand break repair via break-induced replication / locomotion / replication fork protection complex / pronucleus / mitotic DNA replication initiation / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / mitotic sister chromatid cohesion / DNA duplex unwinding / DNA unwinding involved in DNA replication / replication fork processing / DNA replication origin binding / mitotic sister chromatid segregation / DNA replication initiation / condensed chromosome / DNA helicase activity / meiotic cell cycle / helicase activity / DNA-templated DNA replication / single-stranded DNA binding / chromosome / nervous system development / DNA helicase / DNA replication / hydrolase activity / cell cycle / cell division / DNA repair / chromatin binding / positive regulation of cell population proliferation / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Donson / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Timeless / Timeless, N-terminal / Timeless protein / CDC45 family / CDC45-like protein / DNA replication complex GINS protein Psf2 ...Donson / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / Timeless / Timeless, N-terminal / Timeless protein / CDC45 family / CDC45-like protein / DNA replication complex GINS protein Psf2 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein timeless homolog / Downstream Neighbor of SoN homolog / DNA replication licensing factor MCM7 / Probable DNA replication complex GINS protein PSF2 / DNA replication licensing factor mcm-6 / DNA replication licensing factor mcm-5 / Probable DNA replication complex GINS protein PSF1 / Cell division control protein 45 homolog / DNA replication licensing factor mcm-4 / DNA replication complex GINS protein PSF3 ...Protein timeless homolog / Downstream Neighbor of SoN homolog / DNA replication licensing factor MCM7 / Probable DNA replication complex GINS protein PSF2 / DNA replication licensing factor mcm-6 / DNA replication licensing factor mcm-5 / Probable DNA replication complex GINS protein PSF1 / Cell division control protein 45 homolog / DNA replication licensing factor mcm-4 / DNA replication complex GINS protein PSF3 / Protein TIPIN homolog / DNA replication complex GINS protein SLD5 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsJenkyn-Bedford M / Yeeles JTP / Labib KPM
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Cancer Research UK United Kingdom
CitationJournal: Science / Year: 2023
Title: DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in .
Authors: Yisui Xia / Remi Sonneville / Michael Jenkyn-Bedford / Liqin Ji / Constance Alabert / Ye Hong / Joseph T P Yeeles / Karim P M Labib /
Abstract: Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that ...Assembly of the CMG (CDC-45-MCM-2-7-GINS) helicase is the key regulated step during eukaryotic DNA replication initiation. Until now, it was unclear whether metazoa require additional factors that are not present in yeast. In this work, we show that DNSN-1, the ortholog of human DONSON, functions during helicase assembly in a complex with MUS-101/TOPBP1. DNSN-1 is required to recruit the GINS complex to chromatin, and a cryo-electron microscopy structure indicates that DNSN-1 positions GINS on the MCM-2-7 helicase motor (comprising the six MCM-2 to MCM-7 proteins), by direct binding of DNSN-1 to GINS and MCM-3, using interfaces that we show are important for initiation and essential for viability. These findings identify DNSN-1 as a missing link in our understanding of DNA replication initiation, suggesting that initiation defects underlie the human disease syndrome that results from DONSON mutations.
History
DepositionApr 25, 2023-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17204.png

Downloads & links

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Map

FileDownload / File: emd_17204.map.gz / Format: CCP4 / Size: 120.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 316 pix.
= 409.22 Å		1.3 Å/pix.
x 316 pix.
= 409.22 Å		1.3 Å/pix.
x 316 pix.
= 409.22 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.295 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0128
Minimum - Maximum-0.020005688 - 0.04868947
Average (Standard dev.)0.00017475456 (±0.0015006426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions316316316
Spacing316316316
CellA=B=C: 409.22 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map 2. Cryo-EM density map of the Caenorhabditis...

Fileemd_17204_half_map_1.map
AnnotationHalf-map 2. Cryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1. Cryo-EM density map of the Caenorhabditis...

Fileemd_17204_half_map_2.map
AnnotationHalf-map 1. Cryo-EM density map of the Caenorhabditis elegans complex CMG helicase/TIM-1/TIPN-1/DNSN-1 dimer on fork DNA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNS...

EntireName: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)
Components
  • Complex: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)
    • Protein or peptide: DNA replication licensing factor MCM2
    • Protein or peptide: DNA replication licensing factor MCM3
    • Protein or peptide: DNA replication licensing factor mcm-4
    • Protein or peptide: DNA replication licensing factor mcm-5
    • Protein or peptide: DNA replication licensing factor mcm-6
    • Protein or peptide: DNA replication licensing factor MCM7
    • Protein or peptide: Probable DNA replication complex GINS protein PSF1
    • Protein or peptide: Probable DNA replication complex GINS protein PSF2
    • Protein or peptide: DNA replication complex GINS protein PSF3
    • Protein or peptide: DNA replication complex GINS protein SLD5
    • Protein or peptide: Cell division control protein 45 homolog
    • Protein or peptide: Downstream Neighbor of SoN homolog
    • DNA: DNA Leading Strand Template
    • Protein or peptide: Protein timeless homolog
    • Protein or peptide: Protein TIPIN homolog
    • DNA: DNA Lagging Strand Template
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNS...

SupramoleculeName: Complex of CMG helicase bound to TIM-1/TIPN-1 and homodimeric DNSN-1 on fork DNA (Caenorhabditis elegans)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 99.448586 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MADRANNDDD VDRQPLPIAD DADDDVDGID EMFNNEDEDP EDEEGENLFG DDMERDYREQ PELDQYSESG MDDASDVGSL SVSARRAAE REMAQRDQLL DDDALMYEDG DSEEVDTRRR GRGRRGRGDA ADDDSVPMEE EDIPVDILEN IRGRTIRDHV S DEAVAKEI ...String:
MADRANNDDD VDRQPLPIAD DADDDVDGID EMFNNEDEDP EDEEGENLFG DDMERDYREQ PELDQYSESG MDDASDVGSL SVSARRAAE REMAQRDQLL DDDALMYEDG DSEEVDTRRR GRGRRGRGDA ADDDSVPMEE EDIPVDILEN IRGRTIRDHV S DEAVAKEI ERRFKNFLRS FHEPGNKQTK YIQMIKSMAA DNRESLEVSF TDLSDDNGEQ NISYFLPEAP NEMLAIMDRA AT EVVMNMY PFYSRVCNEI KVRISQLPVE EDIRMLRQVH LNMLIRTAGV VTIASGILPQ LAVVKYDCVA CGYLLGPFVQ QND EEVRPT ICPSCQGKGP FELNVENTVY HNYQRITMQE SPNKVAAGRL PRSKDVILLG DLCDSCKPGD EIEVTGVYTN NFDG SLNYK QGFPVFNTLI HANHITNKDK MASDQLTDED IKAIRELSQD PNISQRVFSS IAPSIYGHDD VKRAIALALF RGEAK NPGA KHRLRGDINV LLCGDPGTAK SQFLRYAAHI APRSVLTTGQ GASAVGLTAY VQRHPVTREW TLEAGAMVLA DKGVCL IDE FDKMSDQDRT SIHEAMEQQS ISISKAGIVT SLHARCTVIA ASNPIGGRYN PTRTFAENVD LTEPILSRFD VLCVIRD SV DSVEDERLAK FVVGNHRTHH PDAKKIVKEG DELEEDQMDE RTGVRLIPQD LLRKYIIYAR EKCHPTLPEQ HSEKFSNI F AQMRKESMAT GSVAITVRHV ESMIRLSEAH AKLHLRSYVN DEDCAAAIRV MLESFVNTQK ASIMRMMKKT FSRHLTENR SANELLLFIL KQLIRQQMHY ATARAAAGTI LQSVTIPESE FIEKAQQLRI ENVKPFYTSE IFASNNFLYD PSKKTIVQEI F

UniProtKB: DNA replication licensing factor MCM2

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Macromolecule #2: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 90.810664 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDGQADGMFI DRAEDARKQE ITEQYLNFLD NQADTFHYRQ KIVKMMNDGE SRLVMNLDEI REILPERAEG LLTQSVLEMN CLQSALQMA INRSDVQAVV KTGFHVGFEG TFGERHVNPR TLKSSYLGNL VCCEGIVTKC STVRQKLLTS VHYCPATNKV L EKKFADFT ...String:
MDGQADGMFI DRAEDARKQE ITEQYLNFLD NQADTFHYRQ KIVKMMNDGE SRLVMNLDEI REILPERAEG LLTQSVLEMN CLQSALQMA INRSDVQAVV KTGFHVGFEG TFGERHVNPR TLKSSYLGNL VCCEGIVTKC STVRQKLLTS VHYCPATNKV L EKKFADFT MLDTAVTNNN YPTEDENKNP LETEFGHSVY KDHQTFTIQE LPESAPAGQL PRAVDCVADL DLADRVKPGD RV RIIGVFR VLPNKQNGVS SGSFRSIIII NHIQMLSKEV IPNFEPQDVK DVRKISKSRN PFELLARSLA PSICGHEETK KAL LCLLLG GMEKILNNGS RLRGDINVLL IGDPSVAKSQ LLRYVLRMAP RAITTTGRGS SGVGLTAAVT TDPDSGERRL EAGA MVLAD RGVVCIDEFD KMSDIDRTAI HEVMEQGRVT ISKAGIHAKL NARCSVLAAA NPVYGRYNPF KSPMENIGMQ DSLLS RFDL IFVLLDEHDA DKDANVAEHV LKLHTYRTQG EADGTVLPMG GGVETISTIN METKKASSSI YEENTQWAGI QDTKIL TMD FMRKYIHLAR SVQPKLTDEA TEYISEVYAD IRSFDITKTD QERTMPVTAR QLETLIRLST AIAKARFSKK VEREDTE KA YNLLHFACFK EKPKARQEYE KKKRAPRIDG DDDEDQSDNE DMATSEEPQS SSVPTAATPR RGVRRRAEDD DSQDSMMD T TIGESQPTAK KARTGPAAIG VDRYKELRKY VRKAFDDIGS TDDMVELQII TDSVQTQAGS HKFTEDELKA GYEQLENDN AAMIAEDKIT LI

UniProtKB: DNA replication licensing factor MCM3

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Macromolecule #3: DNA replication licensing factor mcm-4

MacromoleculeName: DNA replication licensing factor mcm-4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 91.687555 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MPRSNDPAEP QSESADLFAE PSSQHSSMRS GSEQVAGNMS PRSTSSASAL QYGSEMGSVS QMSSASTLRR GGPRGDLGIA AVDHRTVQI RGMEDEMAGD DGQPRLYVWG TRICVADVQR SFRDFLTTFK ISQLAEDENM MTGHDEALHE IDVNHPYYME R LLECNDAE ...String:
MPRSNDPAEP QSESADLFAE PSSQHSSMRS GSEQVAGNMS PRSTSSASAL QYGSEMGSVS QMSSASTLRR GGPRGDLGIA AVDHRTVQI RGMEDEMAGD DGQPRLYVWG TRICVADVQR SFRDFLTTFK ISQLAEDENM MTGHDEALHE IDVNHPYYME R LLECNDAE VTHINLNLKH LNAFSEALYR KVIAYPADVI PYLDIVVNEV FAERFNRTLA QSIELRPFNA QKTRNMRGLN PN DVDQLIT ISGMVTRTSS LIPEMRSGYF QCAVCAFGIE SEVDKGRIEE PVVCTNCSNT HCFQLVHNRS VFLDKQVVKL QES PDDMPS GETPHTVSVY AHGSLVESVQ PGDRITVTGI FRATGMKVNP KQRALASVYR TSIDALHFRK MDTSRLHQDN GETI TEERI QQIIELSKRP DIMDALAQSI APSIYEHDDV KRGLLCLLFG GTRKDDETTN KTKLRSEINI LLCGDPGTSK SQMLQ YVYR LLPRSQYTSG KGSSAVGLTA SVSRDADTKQ LVLQTGALVL ADNGVCCIDE FDKMNESARS VLHEVMEQQT LSIAKA GII CQLNARASVL AAANPVDSKW NRNKTIVENI TLPHTLLSRF DLIFLIVDAQ DEMQDRRLGN HLVSLYFEND GNQEKTE HV DMNLLRDYIA YAKANIHPKL SEEASQFIIE KYLFMRKAGA QHGQITAYPR QLESLIRLSE AHAKIRLSQE VSVDDVEK A FTLWREALKQ SAVDPSTGRV DVAILASGMS ASGRKAVEAM CEAVLKQLKT AKGFVTSKAL FHTLKSADKT CQREVFDEA INELSKKESI ARSGDRIRFQ TEA

UniProtKB: DNA replication licensing factor mcm-4

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Macromolecule #4: DNA replication licensing factor mcm-5

MacromoleculeName: DNA replication licensing factor mcm-5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 85.057734 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSNLDNPGIY YQERFFANDG VPDTGRELIA EYRQLITQFR NFIRDFSTGG FGMIYRDQLK RNYFSHEYRL EINLNHLKNF DEDIEMKLR KFPGKVLPAL EEAAKIVADE ITTPRPKGEE KLHDIQVTLT LDEYPTSLRQ VKSAQVSQVV KISGIIVAAA Q VRSKATKV ...String:
MSNLDNPGIY YQERFFANDG VPDTGRELIA EYRQLITQFR NFIRDFSTGG FGMIYRDQLK RNYFSHEYRL EINLNHLKNF DEDIEMKLR KFPGKVLPAL EEAAKIVADE ITTPRPKGEE KLHDIQVTLT LDEYPTSLRQ VKSAQVSQVV KISGIIVAAA Q VRSKATKV TLQCRQCKHT IPDVSIKPGL EGFALPRTCA APQQGQMQRC PIDPYIMLPD KCECVDYQTL KLQENPEDVP HG EMPRHLQ LFTERYLTDK VVPGNRVTIV GVYSIKKLIQ KKGGDKSLQG IRTPYLRVLG IHMETSGPGR TNFTTFTPEE ERM FKTLAQ RKDAYELIAK SIAPSIYGSA DIKKSIACLL FGGARKKLPD GITRRGDINV LLLGDPGTAK SQLLKFVEQV SPIG VYTSG KGSSAAGLTA SVIRDPQSRS FIMEGGAMVL ADGGVVCIDE FDKMREDDRV AIHEAMEQQT ISIAKAGITT TLNSR CSVL AAANSVYGRW DESRGDDNID FMPTILSRFD MIYIVKDTHD VLKDATLAKH VIEVHVNASA AKERDIAGVP KTATTD SDG VMTMFDTDGF LTIEFLKKFV TYARLNCGPR LTPQASEKLV NHYVKMRNPV VNADAFKSGK KAHNSAIPIT VRQLEAI VR IAESIAKMEL QQFATDKHVE EALRLFRVST IEAAATGNLA GVEGFTSTAD QEALNRIEVQ MKKRFAIGTH VSEHLIVQ D FVARQHYRES LVKKVIDNLV RRGDLQQKMQ RKMLYRVR

UniProtKB: DNA replication licensing factor mcm-5

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Macromolecule #5: DNA replication licensing factor mcm-6

MacromoleculeName: DNA replication licensing factor mcm-6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 91.24832 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDNIIGGQAQ QVEDTDGTRV QNEFSKFLKS FKDQKNEFIY KSAMKELVQP EKNTIFINMQ HLYKFSNNLA TTIELQYYRV YPFMCEALH LATLDACDES ERQQMFKKQL YVSLFNLDAK TKVRELSADK VGGLVRIAGQ IVRTHPVHPE LSRACFVCED C GVTTRDVQ ...String:
MDNIIGGQAQ QVEDTDGTRV QNEFSKFLKS FKDQKNEFIY KSAMKELVQP EKNTIFINMQ HLYKFSNNLA TTIELQYYRV YPFMCEALH LATLDACDES ERQQMFKKQL YVSLFNLDAK TKVRELSADK VGGLVRIAGQ IVRTHPVHPE LSRACFVCED C GVTTRDVQ QQFRYTQPTK CANPQCMNRT RFSLDVNSST FVDFQKIRIQ ETQAELPRGS IPRTVDVIVR GEMVETVQPG DK CDIVGTL IVIPDIAQLS TPGLRAETSN QNRGRATDKS EGITGLKALG VRDLTYKMAF LACHIQQTES LVGGDASGAV EET DYLDLW SKMSTEDRAT LKKMSDDKKI EKNIVDSLFP NIYGNHEVKL GVLLMLLGGV AKKSRDEGTS LRGDINVCLV GDPS TAKSQ VLKAVEEFSP RAIYTSGKAS SAAGLTAAVV KDEESFEFVI EAGALMLADN GVCCIDEFDK MDLKDQVAIH EAMEQ QTIS ITKAGVKATL NARASILAAA NPVNGRYDRS RPLKYNVQMS APIMSRFDLF FVLVDECNEV TDYAIARRIL DNHRAI SEH TERDSVYKID DIKKYIAFAR CFKPKISDKA AETLVREYKK LRMSDSNNAA TSSWRITVRQ LESLVRLSEA LARLHCG KE VLVEHVEKAA ELLNKSIVRV EQPDIALDDD DFDNNIMVVE ADKENQRGDD SMDHDGEKEN APKIDIAKLK ISFKEYKQ L SDVLVLHMRS DEDNQGEDEY DGVKQSALVE WYLSTIEADL ETEEDFNVQK TICERVIHRL IHQDHVLLEV EQGEDPTLC VHPNYVIADE

UniProtKB: DNA replication licensing factor mcm-6

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Macromolecule #6: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 81.721352 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKTTTYNTDW AAEKTKIRSF FDEYYVDNED GSGKAFPYRD QVFEIARRDK QAIVVNVDHI KESDIPDALE LSEAITSNTK RYEVLFKDT ISDMIQDYLG DKQAPVIDAL DAYMFQRLHM DRNEGAANEE VSLQDKRKKY PPQLLQRFEV YFTTDDAAHE T CVRNIKAT ...String:
MKTTTYNTDW AAEKTKIRSF FDEYYVDNED GSGKAFPYRD QVFEIARRDK QAIVVNVDHI KESDIPDALE LSEAITSNTK RYEVLFKDT ISDMIQDYLG DKQAPVIDAL DAYMFQRLHM DRNEGAANEE VSLQDKRKKY PPQLLQRFEV YFTTDDAAHE T CVRNIKAT EIGHLVSMKG VVIRATEVKP CVEVMTYTCD TCAAEVYQPV KGMQFTPPVN CPNKECVEAK ANGRLHMQLR GS KFVKFQE LKIQELSEQV PVGSIPRTMT VHVYGEMTRK CNTGNVVHVS GVFLPIMQSG FRPTGGLVAD TYLEAHYINN LDD NPTFNG VQSAELEVLR RKGDNYETLA ASIAPEIFGH VDVKKCLLMA LVGGNDNSSN GMKIRGCINV LMMGDPGVAK SQLL GYVNR LAPRSQYTTG RGSSGVGLTA AVMKDPVTGE MSLEGGALVL ADGGICCIDE FDKMMDHDRT AIHEVMEQQT ISIAK AGIM TTLNARTAII AAANPAYGRY NPNRSIEQNV DLPAALLSRF DLILLMQDKA DRENDKILAE HITYVHQHGC HPNREK KDL ISLETLREYI SLCKTYTPTV DPALRERIVE AYVEMRRDAR YSSDPTFVSP RMILGIVRMA TARAKLRLST IVDESDV EE ALRLMQFAKD SLRPEQNKIE KRMAPVDAAF AVLRELYHAD NAPIAISNAI QRCARKGISE VALKKCLDQY TANGLLVM D RQNIVFAMN

UniProtKB: DNA replication licensing factor MCM7

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Macromolecule #7: Probable DNA replication complex GINS protein PSF1

MacromoleculeName: Probable DNA replication complex GINS protein PSF1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 23.064361 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GPGSMSSGDQ NRGGVADKAL QLVLEMKRNP DVLPPYNTEL VRQCYQKIDE LFQKNAAVVE KIRAGLPHDS TLLQPRLAAM CHIRRCMMA YVNERKNRIR SFRWKYGGAL PASVRNALCD AEIQFFNEYS STLARFQSNL GEGGVNLLLH SAPPKSLFVQ V RALEDYGE ...String:
GPGSMSSGDQ NRGGVADKAL QLVLEMKRNP DVLPPYNTEL VRQCYQKIDE LFQKNAAVVE KIRAGLPHDS TLLQPRLAAM CHIRRCMMA YVNERKNRIR SFRWKYGGAL PASVRNALCD AEIQFFNEYS STLARFQSNL GEGGVNLLLH SAPPKSLFVQ V RALEDYGE FETSDGTQVQ LSKDSLHSLP RQDCEMLIRQ GVLELVH

UniProtKB: Probable DNA replication complex GINS protein PSF1

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Macromolecule #8: Probable DNA replication complex GINS protein PSF2

MacromoleculeName: Probable DNA replication complex GINS protein PSF2 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 20.34933 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MNAERCEFIA GNSLIEVIPS ISDDRPIHLI SGDIGPFEAG VPCRIPVWTA ILMKRKHNCK VVAPQWMDVD ELKKILTSET ESQGLAKLP DHFFEISHML VRDAREDIFE VEAVKSLVQD IYDRRDAKLR SSAIEFLRQN QTCHAQLDNV QLIEASSARA T LEACRQMG AVVRNKHEST PL

UniProtKB: Probable DNA replication complex GINS protein PSF2

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Macromolecule #9: DNA replication complex GINS protein PSF3

MacromoleculeName: DNA replication complex GINS protein PSF3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 21.717668 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAGFEIQRVE SKFFDLDDII AKSDSTSCTF EIGDLNPDFF QEMLGVSKPT QNADGYGVDA PYWLLESVRS SFSIQLPKAY SVNMQNVLN ADSKKLNLSG LQQHFYGNGM QLCRLMKGEN PDGALSLARC LVSTLTQRLG EIVSTATHLQ SKGEKFDSLE T KVFLEGKR ...String:
MAGFEIQRVE SKFFDLDDII AKSDSTSCTF EIGDLNPDFF QEMLGVSKPT QNADGYGVDA PYWLLESVRS SFSIQLPKAY SVNMQNVLN ADSKKLNLSG LQQHFYGNGM QLCRLMKGEN PDGALSLARC LVSTLTQRLG EIVSTATHLQ SKGEKFDSLE T KVFLEGKR CKEDIDTWLR QDNKCSSKKR KRLSL

UniProtKB: DNA replication complex GINS protein PSF3

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Macromolecule #10: DNA replication complex GINS protein SLD5

MacromoleculeName: DNA replication complex GINS protein SLD5 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 25.705123 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAVTDSATTF LDFDDDEYDE MTTPEEVLRK MTATWQNELC APCLLPTQME LVEILLDQIQ GMEENIGKQT DKMQLRISVH RVELQRIGF ITSDYVRCRL QKIESNPHDA IDQHKKRKEE GKSDLLSESE MKFAEEYALA ESNLFQKTVL EFMPAALKKM P VPRGDHDD ...String:
MAVTDSATTF LDFDDDEYDE MTTPEEVLRK MTATWQNELC APCLLPTQME LVEILLDQIQ GMEENIGKQT DKMQLRISVH RVELQRIGF ITSDYVRCRL QKIESNPHDA IDQHKKRKEE GKSDLLSESE MKFAEEYALA ESNLFQKTVL EFMPAALKKM P VPRGDHDD VMVYAKVTSD DVGNVAIPDW QDLNGEVILE MEPESCHLIP FESVHQLVED GNIQLM

UniProtKB: DNA replication complex GINS protein SLD5

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Macromolecule #11: Cell division control protein 45 homolog

MacromoleculeName: Cell division control protein 45 homolog / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 66.245758 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MIIEDNFRQE FYNKIKKGDK SVVLIVSVDT DALCTTMILT HLLRCDDIPF SILAVEGWSS VEKIFADSQE QKCHYILINC GATRSLTRL QIPPASIAFV IDSHRPFHIE NVYENGQIHL LANPSEMSEL QIPDLESVIR EDSDDEEDSD EDEDQEYISY E QRMEKIRR ...String:
MIIEDNFRQE FYNKIKKGDK SVVLIVSVDT DALCTTMILT HLLRCDDIPF SILAVEGWSS VEKIFADSQE QKCHYILINC GATRSLTRL QIPPASIAFV IDSHRPFHIE NVYENGQIHL LANPSEMSEL QIPDLESVIR EDSDDEEDSD EDEDQEYISY E QRMEKIRR KAIKREEMQI WERQRRTILW RYYESTWFSS PSCVTLLEMA AEMNRVSAET MWFTAVGLNS AMADKLISIE MY TQICVDR MRPFVHRFMP KNIVNQGKVD DLLHITFGRE LPLALYSHWD LFSAMMVSEY FSIKTKNWTQ KGDVNIRHLL AQL GITLHE TKQKFEALPT EQRNLVVDVL EKEMDSSFAT FFGTLGYCGK LSACDVARAV TLRLEMPKSE TIMNRFRSGQ SILR SSITG ERQDRLNLNN TFTSICQRTL QVSWKTVAAA INQSEIIPNG PYYLFSCSRS IDEDMVDSRH FLYNTAGFMI RAFAS MKKG RTTKPLIAMF PLTGESAGWL VVTGVMPIAT IYEDSLLKTC IGRAFERVKK MTPPLRIVDD YFNSDIIRLK SEDRTR FID FLQTVFEGTS N

UniProtKB: Cell division control protein 45 homolog

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Macromolecule #12: Downstream Neighbor of SoN homolog

MacromoleculeName: Downstream Neighbor of SoN homolog / type: protein_or_peptide / ID: 12 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 66.079383 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSDEHYNPRN RLKTQIKRRS SCRNILNAVP PPPPTDFEGL EGFTDSCPAP TANNPFKVSS PQKKRQKPQV TFSQDDPFAA SISRSPDPL KTPTKGVRSS PRKRKSPQKF ERFQSFDPAL LQEFHPVDFS ALLATSSSAQ KPAEPAQESA EDLPTDLRIG S KMRIVSKV ...String:
MSDEHYNPRN RLKTQIKRRS SCRNILNAVP PPPPTDFEGL EGFTDSCPAP TANNPFKVSS PQKKRQKPQV TFSQDDPFAA SISRSPDPL KTPTKGVRSS PRKRKSPQKF ERFQSFDPAL LQEFHPVDFS ALLATSSSAQ KPAEPAQESA EDLPTDLRIG S KMRIVSKV SFPWMNTRKS TGNVIVKFQT NDRFDGMQYF NKTFLNGYED PTVPLPVSPM SILEAASLFY QFPVIPGLKM YP RITAEQE NVSRVSLAPL VTSTMLEQWQ ECYAELYSSY KKGQRGSFYV ATAVCNVLFT KMPLSGGGDD VAADDTSQSC SQA FRGQKL VAVITHTTSA IREHLRSQGV DFEAPKPTSS LKRVSSSPQL HHDQSTLDCL LASESKENSQ MGPTTFGGIE NSEN SDESP LKKDQDSDEN ESPMKLANQW LNEIGVSPRT VKNTVSRELS SQVTDRAGFQ CLVVHGSKIH ALFNALMDSD VVHEK TGPY TKIPPTLIAT SPFLYGQLLS LTKSSNIFAK AGTKCTEYEL KLENGPVLPH CAKMMTQFIR STNMCSTEEK PVTMQV MDR HTSQGMSDWT ETATNWNTVT IAENCVKWTK N

UniProtKB: Downstream Neighbor of SoN homolog

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Macromolecule #14: Protein timeless homolog

MacromoleculeName: Protein timeless homolog / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 157.256656 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNVLVQGAVH ALGYYEDGKY SREPDCYESI RDLIRYLRED GDDHTARIEC GRHNLVEQDL VPMVKCEDLT DDEFDIAIRL MVNLCQPAI STMRGKPPAD RDQWKMYWEL EENLRRAKTA FSDAHFFTAI KKRIDNYFID TEYEDRDERL RLVVERIVLL I KYVFSINP ...String:
MNVLVQGAVH ALGYYEDGKY SREPDCYESI RDLIRYLRED GDDHTARIEC GRHNLVEQDL VPMVKCEDLT DDEFDIAIRL MVNLCQPAI STMRGKPPAD RDQWKMYWEL EENLRRAKTA FSDAHFFTAI KKRIDNYFID TEYEDRDERL RLVVERIVLL I KYVFSINP DTSEGRRTRI EDSSHDRVII AFLESGIDKT LMHIANQPRE KEFHVTILDI FALILKEQTA EDLATKSEEV ST AEQKKTE EEFRKIIENH VVKETQKRKS FSRFGGSYTI KGLKGISANS SQVVFKPIQN VEKHNFLDDR KAKKRAPRNR RPF EIDTNS HFASSEVRGM LRDMVIRIIE TCFNRLMKSS KTTVFVQVQK TSQINYFFLI KFVLRFVRLS RQDHLLERIS ECIG VEAFH ENNVQLTEYV ENATTLKGVE AKSHGLKAQY ALGAYNELVL LHRYIYEHAK EENERKFAKR ALEHIVNVEE YRELP IFII KKFSSSVLSN NFLRELVLTT HHYMKLVERF VKTGALKKVT KKVKVRKATK KSKMSEEDVR SEFDGMSKKD LDRLWE ESK GLVLQILKKE VPEMRGMNPI DSQLDVPVDA QQKFAKLSIQ RSLRSRGFPA AVGLYHASRA LWPESFKRGL TDFQDSP GE EDQLQELEQL LKADMKKVAK DLKKAESCKT CDEDPAYKKY DKMDATALQS LWEQSTDTLA RILSHELPES ESTSPVNW Q LDITPDVQQK FAMLAIQRAL RARDLPAAVG LYHTSRKLWP GDEAIFGAPG IGVEEEIAEL KAILEADLHE VAREMKVAE DRAEDPDEED PAEPYDSEQE EEEEVPAWKV EEIDFQFDSY VCKFSNVDVL KWYVFLLNDF SKNSTELNQA LVKMLHRIAF DLKLPIKLY QVSLFQVFSK VNEHFTHLSK DLRKSSRLYE LYQFGFHLLK KFFSKFTGDL AIEALFWKGP RECFEIENGY G SWVKSREA DIRVWTEDLE IELRNLYEEY RTMETRDGID VLDFIEHNLS RARSRKKVAK KLIEFGFDLL GAKWKNSDKA RM DSVLPIG DIQKWYDEWK EAGARGDLVN VLQEKLNEDL GMEISRKKIL KQLAHMDILY EKPKKEKPLP QWDTGLIEEL KKL KEQYDD IPDALNMLGV NIVRYVMKRL SEKKPTRQVE RHLESLGATI PERSKKSEKN GKKFDDFLND DDDDSENDVG GGSE DDEEE EIVMKSKRII PDSEDEEEHI EQEEAQKKLE KVAEKPNTLM GMIAGRKRKL AQLESDSSDE SDDDDSAEKE EKKLP AAED DSDLEEDAVI YKRSYVDALL TGGSIAGNGI TETRRDTSEE REDDDDEDPF TKKLTFKRRI VMSDNEDEA

UniProtKB: Protein timeless homolog

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Macromolecule #15: Protein TIPIN homolog

MacromoleculeName: Protein TIPIN homolog / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 27.415215 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GPGSMDEMED FFENDELDRE PSPMGDEAIE DNSGEGGTRR VVEPKLLRTK RLANPRLALN ERILTGPKGI SALRETLKDF KPNPKDDPY ANLEKLMKKY AYWGHLMFPK MKTEDVLNRV ETLGTRRQVK VFMIKHRLGE TGEDSEHEEQ ENQKNGIIDD G ASDNDDDL ...String:
GPGSMDEMED FFENDELDRE PSPMGDEAIE DNSGEGGTRR VVEPKLLRTK RLANPRLALN ERILTGPKGI SALRETLKDF KPNPKDDPY ANLEKLMKKY AYWGHLMFPK MKTEDVLNRV ETLGTRRQVK VFMIKHRLGE TGEDSEHEEQ ENQKNGIIDD G ASDNDDDL FKDLPEKEVT TEKAKNSEKS DQKTAEIDEN VEEEYRMMEE ERLREEQEAK EAADEDALME DFGDMNNDW

UniProtKB: Protein TIPIN homolog

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Macromolecule #13: DNA Leading Strand Template

MacromoleculeName: DNA Leading Strand Template / type: dna / ID: 13 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.396836 KDa
SequenceString: (DT)(DA)(DG)(DA)(DG)(DT)(DA)(DG)(DG)(DA) (DA)(DG)(DT)(DG)(DA)(DT)(DG)(DG)(DT)(DA) (DA)(DG)(DT)(DG)(DA)(DT)(DT)(DA)(DG) (DA)(DG)(DA)(DA)(DT)(DT)(DG)(DG)(DA)(DG) (DA) (DG)(DT)(DG)(DT)(DG)(DT) ...String:
(DT)(DA)(DG)(DA)(DG)(DT)(DA)(DG)(DG)(DA) (DA)(DG)(DT)(DG)(DA)(DT)(DG)(DG)(DT)(DA) (DA)(DG)(DT)(DG)(DA)(DT)(DT)(DA)(DG) (DA)(DG)(DA)(DA)(DT)(DT)(DG)(DG)(DA)(DG) (DA) (DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)

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Macromolecule #16: DNA Lagging Strand Template

MacromoleculeName: DNA Lagging Strand Template / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.524887 KDa
SequenceString: (DG)(DG)(DC)(DA)(DG)(DG)(DC)(DA)(DG)(DG) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DC)(DT)(DC)(DT)(DC)(DC)(DA)(DA)(DT) (DT)(DC)(DT)(DC)(DT)(DA)(DA)(DT)(DC)(DA) (DC) (DT)(DT)(DA)(DC)(DC)(DA) ...String:
(DG)(DG)(DC)(DA)(DG)(DG)(DC)(DA)(DG)(DG) (DC)(DA)(DG)(DG)(DC)(DA)(DC)(DA)(DC)(DA) (DC)(DT)(DC)(DT)(DC)(DC)(DA)(DA)(DT) (DT)(DC)(DT)(DC)(DT)(DA)(DA)(DT)(DC)(DA) (DC) (DT)(DT)(DA)(DC)(DC)(DA)(DT)(DC) (DA)(DC)(DT)(DT)(DC)(DC)(DT)(DA)(DC)(DT) (DC)(DT) (DA)

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #19: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 19 / Number of copies: 4 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: CONTINUOUS / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.7 sec. / Average electron dose: 40.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10619

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33900

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